vg
vg copied to clipboard
Published
20 hours ago •
vgteam
vgteam
vg call crashed with activated nested calling mode
1. What were you trying to do? run vg call to get vcf
2. What did you want to happen? get all level variants, no matter top level or nested
3. What actually happened? vg call crashed
4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
━━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━━━━━━━vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
v1.52.0 "Bozen"
━━━━━━━━━vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
━━━━━━vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
━━vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
━━━━━━━━━vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
━vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
━━━━━━━━━vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
━━━━━━━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
━
Crash report for vg v1.52.0 "Bozen"
━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
v1.52.0 "Bozen"
━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
━━━━━━━━━━━━━━━━━━━━━━━━━
Crash report for vg vg: src/graph_caller.cpp:2063: bool vg::NestedFlowCaller::call_snarl_recursive(const vg::Snarl&, int, const string&, std::pair<long unsigned int, long unsigned int>, vg::NestedFlowCaller::CallTable&): Assertion `false' failed.
━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━━━━━━━
Crash report for vg ━━v1.52.0 "Bozen"
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
━━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
v1.52.0 "Bozen"
━━━━━━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
━━━━━━━━━━━━━━━v1.52.0 "Bozen"
━━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━
Crash report for vg v1.52.0 "Bozen"
v1.52.0 "Bozen"
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
v1.52.0 "Bozen"
━━━━━
Crash report for vg v1.52.0 "Bozen"
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last)Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
Stack trace (most recent call last) in thread 31667:
##13 Object "", at 0xffffffffffffffff, in
#13 Object "", at 0xffffffffffffffff, in
#12 Object "", at 0x1fb7902, in
#11 Object "", at 0x14b98e8, in
#10 Object "", at 0x1eec109, in
##13 Object "", at 0xffffffffffffffff, in
#12 Object "", at 0x1fb7902, in
#11 Object "", at 0x14b98e8, in
#10 Object "", at 0x1eec109, in
#9 Object "", at 0x1eee9d7, in
#8 Object "", at 0x1ee609b, in
#13 Object "", at 0xffffffffffffffff, in
#13 Object "", at 0xffffffffffffffff, in
in thread 31667:
#13 Object "", at 0xffffffffffffffff, in
9 Object "", at 0x1eee9d7, in
#13 Object "", at 0xffffffffffffffff, in
#13 Object "", at 0xffffffffffffffff, in
#13 Object "", at 0xffffffffffffffff, in
Stack trace (most recent call last) in thread 31667:
#13 Object "", at 0xffffffffffffffff, in
#13 Object "", at 0xffffffffffffffff, in
#13 Object "", at 0xffffffffffffffff, in
#13 Object "", at 0xffffffffffffffff, in
Stack trace (most recent call last) in thread 31667:
#13 Object "", at 0xffffffffffffffff, in
#13 Object "", at 0xffffffffffffffff, in
#13 Object "", at 0xffffffffffffffff, in
Stack trace (most recent call last) in thread 31667:
#13 Object "", at 0xffffffffffffffff, in
#13 Object "", at 0xffffffffffffffff, in
13 Object "", at 0xffffffffffffffff, in
#13 Object "", at 0xffffffffffffffff, in
#13 Object "", at 0xffffffffffffffff, in
Stack trace (most recent call last) in thread 31667:
#13 Object "", at 0xffffffffffffffff, in
#13 Object "", at 0xffffffffffffffff, in
Stack trace (most recent call last) in thread 31667:
#13 Object "", at 0xffffffffffffffff, in
##12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
##12 Object "/vg/bin/vg", at 0x1fb7902#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
12 Object "/vg/bin/vg", at #12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
#12 Object "/vg/bin/vg", at 0x1fb7902, in __clone
0x1fb7902, in __clone
#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread#11 Object "/vg/bin/vg", at #11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread##11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
0x14b98e8, in start_thread
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#11 Object "/vg/bin/vg", at #11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#11 Object "/vg/bin/vg", at 0x14b98e8#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
0x14b98e8, in start_thread
, in start_thread
#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#11 Object "/vg/bin/vg", at 0x14b98e8, in start_thread
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#6 Object "/vg/bin/vg", at 0x100c392, in std::_Function_handler<void (vg::Snarl const*), vg::GraphCaller::call_top_level_snarls(handlegraph::HandleGraph const&, vg::GraphCaller::RecurseType)::{lambda(vg::Snarl const*)#1}>::_M_invoke(std::_Any_data const&, vg::Snarl const*&&)
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#10 Object "/vg/bin/vg", at 0x1eec109, in #10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
gomp_thread_start
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#6 Object "/vg/bin/vg", at 0x100c392, in std::_Function_handler<void (vg::Snarl const*), vg::GraphCaller::call_top_level_snarls(handlegraph::HandleGraph const&, vg::GraphCaller::RecurseType)::{lambda(vg::Snarl const*)#1}>::_M_invoke(std::_Any_data const&, vg::Snarl const*&&)
#10 Object "#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#5 Object "/vg/bin/vg", at 0x10208a3, in vg::NestedFlowCaller::call_snarl(vg::Snarl const&)
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
#10 Object "/vg/bin/vg#10 Object "/vg/bin/vg", at 0x1eec109, in gomp_thread_start
", at 0x1eec109, in gomp_thread_start
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7#4 Object "/vg/bin/vg", at 0x1020708, in vg::NestedFlowCaller::call_snarl_recursive(vg::Snarl const&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::pair<unsigned long, unsigned long>, std::map<vg::Snarl, vg::NestedFlowCaller::CallRecord, vg::NestedCachedPackedTraversalSupportFinder::snarl_less, std::allocator<std::pair<vg::Snarl const, vg::NestedFlowCaller::CallRecord> > >&)
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#5 Object "/vg/bin/vg", at 0x10208a3, in vg::NestedFlowCaller::call_snarl(vg::Snarl const&)
#9 Object "/vg/bin/vg", at 0x1eee9d7, in #9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7, in gomp_team_barrier_wait_end
#9 Object "/vg/bin/vg", at 0x1eee9d7#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
, in gomp_team_barrier_wait_end
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#3 Object "/vg/bin/vg", at 0x1f0f655, in __assert_fail
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#4 Object "/vg/bin/vg", at 0x1020708, in vg::NestedFlowCaller::call_snarl_recursive(vg::Snarl const&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::pair<unsigned long, unsigned long>, std::map<vg::Snarl, vg::NestedFlowCaller::CallRecord, vg::NestedCachedPackedTraversalSupportFinder::snarl_less, std::allocator<std::pair<vg::Snarl const, vg::NestedFlowCaller::CallRecord> > >&)
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#8 Object "/vg/bin/vg", at 0x1ee609b, in gomp_barrier_handle_tasks
#6 Object "/vg/bin/vg", at 0x100c392, in std::_Function_handler<void (vg::Snarl const*), vg::GraphCaller::call_top_level_snarls(handlegraph::HandleGraph const&, vg::GraphCaller::RecurseType)::{lambda(vg::Snarl const*)#1}>::_M_invoke(std::_Any_data const&, vg::Snarl const*&&)
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#3 Object "/vg/bin/vg", at 0x1f0f655, in __assert_fail
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#2 Object "/vg/bin/vg", at 0x5c25f7, in __assert_fail_base.cold
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#5 Object "/vg/bin/vg", at 0x10208a3, in vg::NestedFlowCaller::call_snarl(vg::Snarl const&)
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#7 Object "/vg/bin/vg#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#1 Object "/vg/bin/vg", at 0x5c2727, in abort
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#4 Object "/vg/bin/vg", at 0x1020708, in vg::NestedFlowCaller::call_snarl_recursive(vg::Snarl const&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::pair<unsigned long, unsigned long>, std::map<vg::Snarl, vg::NestedFlowCaller::CallRecord, vg::NestedCachedPackedTraversalSupportFinder::snarl_less, std::allocator<std::pair<vg::Snarl const, vg::NestedFlowCaller::CallRecord> > >&)
#7 Object "/vg/bin/vg", at 0xfe6e2e, in vg::SnarlManager::for_each_top_level_snarl_parallel(std::function<void (vg::Snarl const*)> const&) const [clone ._omp_fn.1]
#6 Object "/vg/bin/vg", at 0x100c392, in std::_Function_handler<void (vg::Snarl const*), vg::GraphCaller::call_top_level_snarls(handlegraph::HandleGraph const&, vg::GraphCaller::RecurseType)::{lambda(vg::Snarl const*)#1}>::_M_invoke(std::_Any_data const&, vg::Snarl const*&&)
#2 Object "/vg/bin/vg", at 0x5c25f7, in __assert_fail_base.cold
#6 Object "/vg/bin/vg", at 0x100c392, in std::_Function_handler<void (vg::Snarl const*), vg::GraphCaller::call_top_level_snarls(handlegraph::HandleGraph const&, vg::GraphCaller::RecurseType)::{lambda(vg::Snarl const*)#1}>::_M_invoke(std::_Any_data const&, vg::Snarl const*&&)
#0 Object "/vg/bin/vg", at 0x14bd16b, in raise
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Please include this entire error log in your bug report!
━━━━━━━━━━━━━━━━━━━━
#3 Object "━━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
━━━━━━━━━━━━━━━━━━━━
Crash report for vg ━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
Stack trace (most recent call last) in thread Stack trace (most recent call last) in thread 31668:
#22 Object "", at 0xffffffffffffffff, in
/vg/bin/vg", at /local/var/spool/slurmd/job12814770/slurm_script: line 107: 31604 Segmentation fault apptainer exec -e -B /home -B /scratch -B /project /home/maxine91/container/vg_v1.52.0.sif vg call ${gbz_file} -k ${pack_file} -r ${snarls_file} -s ${sample_name} -t $SLURM_CPUS_PER_TASK -z -a -n > ${vcf_file}
5. What data and command can the vg dev team use to make the problem happen? command:
vg call ${gbz_file} \
-k ${pack_file} \
-r ${snarls_file} \
-s ${sample_name} \
-t $SLURM_CPUS_PER_TASK \
-z -a -n \
> ${vcf_file}
6. What does running vg version say?
vg version v1.52.0 "Bozen"
Compiled with g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 on Linux
Linked against libstd++ 20210601
Built by root@buildkitsandbox
